 
####################################################### 
#                                                     # 
#                        ACE                          # 
#                                                     # 
#        Ab-initio protein structure prediction       # 
#                         &                           # 
#               Comparative modeling                  # 
#                                                     # 
#                     Evaluator                       # 
#                                                     # 
#                ----------------- 11/1998            # 
#                                                     # 
#                         by                          # 
#           Adam Zemla & Ceslovas Venclovas           # 
#                                                     # 
#         Protein Structure Prediction Center         # 
#      Lawrence Livermore National Laboratory, CA     # 
#                                                     # 
####################################################### 
########################## 
#                        # 
#    ACE parameters:     # 
#                        # 
########################## 
# 
# MEASURES: 
# 
# For AB: 0 3 9 13 14 
# For CM: 0 1 2 3 6 7 8 9 10 11 12 13 14 18 
# 
ARMSMC  0 1 2     7 8 9    11 12 13 14 18 
ARMSSC  0 1 2 3 6 7 8 9    11 12 13 14 18 
# 
CRMSCA  0 1 2     7 8 9 10 11 12 13 14 18 
CRMSMC  0 1 2     7 8 9 10 11 12 13 14 18 
CRMSSC  0 1 2 3 6     9    11 12 13 14 18 
CRMSALL 0 1 2     7 8 9    11 12 13 14 18 
# 
D-E_CA  0 1 2     7 8 9    11 12 13 14 18 
D-E_MC  0 1 2     7 8 9    11 12 13 14 18 
D-E_SC  0 1 2 3 6 7 8 9    11 12 13 14 18 
D-E_ALL 0 1 2     7 8 9    11 12 13 14 18 
# 
# Output parameters 
# 
DIHED-OUTPUT        0         #    1 - ON, 0 - OFF 
RES-CONTACTS        0         #    1 - ON, 0 - OFF 
SS-OUTPUT           1         #    1 - ON, 0 - OFF 
PHI-PSI             0         #    1 - SEPARATELY, 0 - NO  
# 
# Calculation parameters 
# 
SOV-METHOD          1         #    0 - SOV 94,  1 - SOV 
# 
TEMP-FACTOR         30.0      #    Target structure temperature factor cutoff 
ACCESS-CUTOFF       0.20      #    Solvent accessibility cutoff   
ANGLES-CORRECT      30.0      #    target-model  (diff < 30.0)    
DSSP-HELIX          6         #    Secondary Structure subset: helix cutoff  
DSSP-STRAND         3         #    Secondary Structure subset: strand cutoff 
ROTAMERS-LIMIT      30.0      #    target-parent (diff > 30.0) 
ROTATION-MATRIX     0         #    1 - ON, 0 - OFF   
SC-SWAPPING         1         #    1 - ON, 0 - OFF    
SEP-CONTACTS        1         #    Separation interval along the chain 
RESIDUE-CONTACTS    8.0       #    Contact definition between two C-beta atoms 
# 
CRMS-METHOD         1         #    0 - ALL, 1 - CA, 2 - MC+CB, 3 - CA (iter)  
ITER-CUTOFF         2.5       #    DISTANCE cutoff (for CA (iter))  
LCS_GDT             1         #    LCS and GDT calculations (1 - ON, 0 - OFF) 
########################## 
#                        # 
#      ACE results:      # 
#                        # 
########################## 
 
 
 
# WARNING! The number of residues in SS section: 12 , MODEL 12 , TARGET 241 
#          The number of residues possible to evaluate: 12 
 
 
 SECONDARY STRUCTURE PREDICTION: 
       NUM    RES   SS   Prediction   Probability 
 SSP   156     L     E     C             1.00 
 SSP   157     E     E     C             1.00 
 SSP   158     L     E     C             1.00 
 SSP   159     I     E     C             1.00 
 SSP   160     G     E     C             1.00 
 SSP   161     Y     C     C             1.00 
 SSP   162     P     C     C             1.00 
 SSP   163     F     C     C             1.00 
 SSP   164     D     C     C             1.00 
 SSP   165     H     C     C             1.00 
 SSP   166     K     C     C             1.00 
 SSP   167     V     C     C             1.00 
 SSP  BREAK 
 
 NP      - Number of predicted residues 
 PP      - Percent of predicted residues 
 Q3      - Residues predicted correctly (H, E, C) 
 Qhelix  - Residues predicted correctly (HELIX) 
 Qstrand - Residues predicted correctly (STRAND) 
 Qcoil   - Residues predicted correctly (COIL) 
 SOV     - Segment overlap quantity 
 
                     Q3      Qhelix   Qstrand   Qcoil      PP 
 Qindex              58.3       0.0      0.0    100.0      5.0 
 
                     ALL      HELIX    STRAND    COIL      PP 
 SOV observed        48.6     100.0      0.0     83.3      5.0 
 
           Considered    Percent predicted   Percent predicted 
            segments        correctly         as wrong type 
 SEG            1               0.0               0.0 
 
         Number of wrong    Number of wrong 
             breaks             joins 
 B/J            0                 0 
 
  CONFIDENCE (P)     Average     NP    PP/BIN     Q3 
 BIN  0.90 - 1.00      1.00      12    100.0     58.3 
 
 BIN  0.00 - 1.00      1.00      12    100.0     58.3 
 
 
 
 
              predicted        number of target      total number   total number 
                as a         contacts possible in         of             of 
               contact         predicted subset:       contacts       contacts 
            percent  number    percent    number       in target    in prediction 
 CONTACTS:     0.0      0         0.0        0             0              0 
 
 
 
 CONSIDERED - explicitly provided contacts (with positive confidence) or 
              non contacts (with negative confidence) possible to evaluate 
 SEP      - Minimum separation between residues considered 
 NPC      - Number of contacts predicted correctly 
 PC(P)    - Percent of contacts predicted correctly from CONSIDERED in PREDICTION 
 PC(T)    - Percent of contacts predicted correctly from CONSIDERED in TARGET with SEP limit 
 PC(TT)   - Percent of contacts predicted correctly from TOTAL in TARGET with SEP limit 
 
                        CONSIDERED     CONSIDERED       TOTAL          TOTAL 
                      in PREDICTION    in TARGET    in PREDICTION    in TARGET 
 ALL RESIDUES USED          13              13            13            241 
 ALL CONTACTS (< 8.0A)      35              23            35           1230 
 
               in PREDICTION      Predicted correctly          Submitted as        in TARGET 
                CONSIDERED     NPC   PC(P)   PC(T)   PC(TT)    NOT  predicted   CONSIDERED  TOTAL  |   SEP 
 RES CONTACTS        35         18   51.43   78.26    1.46       0     0.00          23      1230  |   1-9999 
 RES CONTACTS        24         18   75.00   78.26    3.12       0     0.00          23       577  |   1-4    
 RES CONTACTS         8          0    0.00    0.00    0.00       0     0.00           0        80  |   5-8    
 RES CONTACTS         3          0    0.00    0.00    0.00       0     0.00           0       573  |   9-9999 
 
 
 
# WARNING! TARGET 1878 atoms, MODEL 1904 atoms, 1876 common with TARGET 
           Number of atoms possible to evaluate: 109 
 
MEASURES: 
 
 
ANGLES RMS : model <-> target 
 
 (MC: PHI+PSI) DIHED RMS:      ARMSMC            PC     NP     PP     TN 
     ALL . . . . . . . . . .    71.31           43.5    23     4.8   480     ARMSMC  
     SECONDARY STRUCTURE . .    64.70           50.0    10     4.6   216     ARMSMC  
     SURFACE . . . . . . . .    78.77           22.2     9     3.8   240     ARMSMC  
     BURIED  . . . . . . . .    66.07           57.1    14     5.8   240     ARMSMC  
 (SC: CHI1) DIHED RMS:         ARMSSC            PC     NP     PP     TN 
     ALL . . . . . . . . . .    86.36           27.3    11     5.4   204     ARMSSC1 
     RELIABLE SIDE CHAINS  .    83.79           30.0    10     5.3   187     ARMSSC1 
     SECONDARY STRUCTURE . .    61.65           50.0     4     4.3    94     ARMSSC1 
     SURFACE . . . . . . . .    96.16           20.0     5     4.9   103     ARMSSC1 
     BURIED  . . . . . . . .    77.25           33.3     6     5.9   101     ARMSSC1 
 (SC: CHI2) DIHED RMS:         ARMSSC            PC     NP     PP     TN 
     ALL . . . . . . . . . .    68.12           60.0    10     6.3   158     ARMSSC2 
     RELIABLE SIDE CHAINS  .    56.19           71.4     7     6.2   113     ARMSSC2 
     SECONDARY STRUCTURE . .    69.38           50.0     4     5.6    72     ARMSSC2 
     SURFACE . . . . . . . .    35.30           75.0     4     4.8    83     ARMSSC2 
     BURIED  . . . . . . . .    83.09           50.0     6     8.0    75     ARMSSC2 
 (SC: CHI3) DIHED RMS:         ARMSSC            PC     NP     PP     TN 
     ALL . . . . . . . . . .    52.14            0.0     2     3.8    52     ARMSSC3 
     RELIABLE SIDE CHAINS  .    52.14            0.0     2     4.3    46     ARMSSC3 
     SECONDARY STRUCTURE . .    34.61            0.0     1     3.7    27     ARMSSC3 
     SURFACE . . . . . . . .    52.14            0.0     2     4.7    43     ARMSSC3 
     BURIED  . . . . . . . .     0.00            0.0     0     0.0     9     ARMSSC3 
 (SC: CHI4) DIHED RMS:         ARMSSC            PC     NP     PP     TN 
     ALL . . . . . . . . . .    14.89          100.0     1     3.4    29     ARMSSC4 
     RELIABLE SIDE CHAINS  .    14.89          100.0     1     3.4    29     ARMSSC4 
     SECONDARY STRUCTURE . .     0.00            0.0     0     0.0    17     ARMSSC4 
     SURFACE . . . . . . . .    14.89          100.0     1     4.3    23     ARMSSC4 
     BURIED  . . . . . . . .     0.00            0.0     0     0.0     6     ARMSSC4 
 
COORDINATES RMS : model <-> target 
 
 
LONGEST_CONTINUOUS_SEGMENT (Longest continuous sequence under CA RMS cutoff   5.00): 
 FRAGMENT  1  155 - 167  13   Length     Seq        L_RMS   ALL_CA_RMS 
  LONGEST_CONTINUOUS_SEGMENT    11    157 - 167      4.77     7.84 
  LCS LOCAL_SCORE:             81.07 
 
 
LONGEST_CONTINUOUS_SEGMENT (Longest continuous sequence under CA RMS cutoff   2.00): 
 FRAGMENT  1  155 - 167  13   Length     Seq        L_RMS   ALL_CA_RMS 
  LONGEST_CONTINUOUS_SEGMENT     6    155 - 160      1.52    14.73 
  LONGEST_CONTINUOUS_SEGMENT     6    159 - 164      1.74     9.82 
  LCS LOCAL_SCORE:             40.83 
 
 
LONGEST_CONTINUOUS_SEGMENT (Longest continuous sequence under CA RMS cutoff   1.00): 
 FRAGMENT  1  155 - 167  13   Length     Seq        L_RMS   ALL_CA_RMS 
  LONGEST_CONTINUOUS_SEGMENT     5    155 - 159      0.92    15.44 
  LONGEST_CONTINUOUS_SEGMENT     5    160 - 164      0.81    11.20 
  LCS LOCAL_SCORE:             34.91 
 
 
 LCS                   LENGTH_OF_THE 
 LCS  RESIDUE  RESIDUE    CONTINUOUS  SECONDARY 
 LCS   NUMBER     NAME       SEGMENT  STRUCTURE   GDT_DATA_COLUMNS (PERCENT OF THE TARGET) 
 LCS     155       K     5    6    8       E        0   1   2   2   2   2   2   2   2   2   2   2   2   3   3   3   3   3   3   3  
 LCS     156       L     5    6    8       E        1   1   2   2   2   2   2   2   2   2   2   2   2   3   3   3   3   3   4   4  
 LCS     157       E     5    6   11       E        1   1   2   2   2   2   2   2   2   2   2   2   3   4   4   4   4   4   4   4  
 LCS     158       L     5    6   11       E        1   1   2   2   2   2   2   2   3   3   3   3   3   4   4   4   4   4   4   4  
 LCS     159       I     5    6   11       E        1   1   2   2   2   2   2   2   3   3   3   3   3   4   4   4   4   4   4   4  
 LCS     160       G     5    6   11       E        1   2   2   2   2   2   2   2   3   3   3   3   3   4   4   4   4   4   4   4  
 LCS     161       Y     5    6   11       C        1   2   2   2   2   2   2   2   3   3   3   3   3   4   4   4   4   4   4   4  
 LCS     162       P     5    6   11       C        1   2   2   2   2   2   2   2   3   3   3   3   3   4   4   4   4   4   4   4  
 LCS     163       F     5    6   11       C        1   2   2   2   2   2   2   2   3   3   3   3   3   4   4   4   4   4   4   4  
 LCS     164       D     5    6   11       C        1   2   2   2   2   2   2   2   3   3   3   3   3   4   4   4   4   4   4   4  
 LCS     165       H     3    3   11       C        1   1   1   1   1   2   2   2   3   3   3   3   3   4   4   4   4   4   4   4  
 LCS     166       K     3    3   11       C        1   1   1   1   1   1   2   2   3   3   3   3   3   4   4   4   4   4   4   4  
 LCS     167       V     3    3   11       C        0   1   1   1   1   1   1   1   2   2   2   2   3   3   4   4   4   4   4   4  
 LCS TOTAL_SCORE (RMS CUTOFF   1.00):   0.10 
 
 NUMBER_OF_CA_Tg:  241      NUMBER_OF_CA_Pr:   13      PERCENT_OF_CA:   5.39  
 
GLOBAL_DISTANCE_TEST (the largest set of residues under DISTANCE_CUTOFF (using LCS results)): 
 GDT DISTANCE_CUTOFF     0.50    1.00    1.50    2.00    2.50    3.00    3.50    4.00    4.50    5.00    5.50    6.00    6.50    7.00    7.50    8.00    8.50    9.00    9.50   10.00  
 GDT NUMBER_OF_CA_max       4       5       5       5       6       6       7       7       8       9       9       9       9      10      11      11      11      11      11      11  
 GDT PERCENT_OF_CA_Pr   30.77   38.46   38.46   38.46   46.15   46.15   53.85   53.85   61.54   69.23   69.23   69.23   69.23   76.92   84.62   84.62   84.62   84.62   84.62   84.62 
 GDT PERCENT_OF_CA_Tg    1.66    2.07    2.07    2.07    2.49    2.49    2.90    2.90    3.32    3.73    3.73    3.73    3.73    4.15    4.56    4.56    4.56    4.56    4.56    4.56 
 GDT FRAGMENT: Beg-End 160-163 160-164 160-164 160-164 155-160 155-160 159-165 159-165 158-166 158-166 158-166 158-166 158-166 157-166 157-167 157-167 157-167 157-167 157-167 157-167 
 GDT RMS_LOCAL           0.37    0.81    0.81    0.81    1.52    1.52    2.51    2.51    3.12    3.34    3.34    3.34    3.34    4.25    4.77    4.77    4.77    4.77    4.77    4.77 
 GDT RMS_ALL_CA         10.89   11.20   11.20   11.20   14.73   14.73    9.10    9.10    8.18    8.32    8.32    8.32    8.32    7.80    7.84    7.84    7.84    7.84    7.84    7.84 
 
 
 TEST (CA)  RMS =   7.21               (Number of atoms:   13) 
 
 (CA)  RMS:                   CRMSCA         NP     PP     TN 
     ALL . . . . . . . . . .    7.21         13     5.4   241     CRMSCA  
     CRN = ALL/NP  . . . . .    0.5549                            CRMSCA  
     SECONDARY STRUCTURE . .    8.29          6     5.6   108     CRMSCA  
     SURFACE . . . . . . . .    8.59          6     5.0   121     CRMSCA  
     BURIED  . . . . . . . .    5.78          7     5.8   120     CRMSCA  
 (MC)  RMS:                   CRMSMC         NP     PP     TN 
     ALL . . . . . . . . . .    7.07         63     5.3  1180     CRMSMC  
     SECONDARY STRUCTURE . .    7.75         28     5.3   533     CRMSMC  
     SURFACE . . . . . . . .    8.34         29     4.9   593     CRMSMC  
     BURIED  . . . . . . . .    5.77         34     5.8   587     CRMSMC  
 (SC)  RMS:                   CRMSSC         NP     PP     TN 
     ALL . . . . . . . . . .    8.43         58     6.3   914     CRMSSC  
     RELIABLE SIDE CHAINS  .    8.44         48     6.3   764     CRMSSC  
     SECONDARY STRUCTURE . .    9.87         22     4.9   449     CRMSSC  
     SURFACE . . . . . . . .    9.92         29     6.3   461     CRMSSC  
     BURIED  . . . . . . . .    6.61         29     6.4   453     CRMSSC  
 (ALL) RMS:                   CRMSALL        NP     PP     TN 
     ALL . . . . . . . . . .    7.77        109     5.8  1878     CRMSALL 
     SECONDARY STRUCTURE . .    8.72         45     5.1   881     CRMSALL 
     SURFACE . . . . . . . .    9.20         52     5.5   945     CRMSALL 
     BURIED  . . . . . . . .    6.17         57     6.1   933     CRMSALL 
 
Accuracy of estimates of atomic coordinate errors: model <-> target 
 
 (CA)  ERRORS:                  |D-E|   |D-E|/|D+E|   SR(D,E)    NP     PP     TN 
     ALL . . . . . . . . . .    2.992      0.251       0.156     13     5.4   241     ERRCA  
     SECONDARY STRUCTURE . .    3.789      0.290       0.201      6     5.6   108     ERRCA  
     SURFACE . . . . . . . .    4.019      0.293       0.148      6     5.0   121     ERRCA  
     BURIED  . . . . . . . .    2.111      0.215       0.162      7     5.8   120     ERRCA  
 (MC)  ERRORS:                  |D-E|   |D-E|/|D+E|   SR(D,E)    NP     PP     TN 
     ALL . . . . . . . . . .    2.843      0.237       0.137     63     5.3  1180     ERRMC  
     SECONDARY STRUCTURE . .    3.305      0.251       0.145     28     5.3   533     ERRMC  
     SURFACE . . . . . . . .    3.933      0.299       0.167     29     4.9   593     ERRMC  
     BURIED  . . . . . . . .    1.913      0.184       0.111     34     5.8   587     ERRMC  
 (SC)  ERRORS:                  |D-E|   |D-E|/|D+E|   SR(D,E)    NP     PP     TN 
     ALL . . . . . . . . . .    4.111      0.320       0.194     58     6.3   914     ERRSC  
     RELIABLE SIDE CHAINS  .    4.056      0.315       0.196     48     6.3   764     ERRSC  
     SECONDARY STRUCTURE . .    5.177      0.354       0.202     22     4.9   449     ERRSC  
     SURFACE . . . . . . . .    5.529      0.393       0.234     29     6.3   461     ERRSC  
     BURIED  . . . . . . . .    2.694      0.247       0.155     29     6.4   453     ERRSC  
 (ALL) ERRORS:                  |D-E|   |D-E|/|D+E|   SR(D,E)    NP     PP     TN 
     ALL . . . . . . . . . .    3.453      0.276       0.163    109     5.8  1878     ERRALL 
     SECONDARY STRUCTURE . .    4.121      0.297       0.172     45     5.1   881     ERRALL 
     SURFACE . . . . . . . .    4.749      0.345       0.197     52     5.5   945     ERRALL 
     BURIED  . . . . . . . .    2.270      0.213       0.133     57     6.1   933     ERRALL 
 
 
 
DISTANCES: Percent of total atoms where distance (target <-> model) in global 
           superposition is less than: 1 , 2 , 3 , 5 , 10 Angstroms 
            D < 1     D < 2     D < 3     D < 5    D < 10      NP      TN 
CA  (N)         0         1         2         5        11      13     241   DISTCA 
CA  (P)      0.00      0.41      0.83      2.07      4.56             241   DISTCA 
CA  (RMS)    0.00      1.81      2.38      3.60      5.59                   DISTCA 
 
ALL (N)         0         5        16        35        87     109    1878   DISTALL 
ALL (P)      0.00      0.27      0.85      1.86      4.63            1878   DISTALL 
ALL (RMS)    0.00      1.54      2.39      3.41      5.80                   DISTALL 
 
 
 
 
END of the results output 
